Merge two PDF files output by LaTeX?

Create the separate documents separately and merge them with a PDF utility. Semantically speaking, I feel this is the way to go rather than futzing with the document settings. After all, what you are submitting is not one "document" but a set of them.

Edit: This is an important question that has been asked more than once. It's also not exactly TeX-related. So I'm community-wikifying my answer so it can be improved and made definitive.

LaTeX

use Herbert's answer: the pdfpages package

documentclass{article}% or something else
usepackage{pdfpages}
begin{document}
includepdf[pages=-]{paper1}
includepdf[pages=-]{paper2}

end{document}

You could also keep the document page sizes by adding a option:

includepdf[pages=-,fitpapaer]{paper1}
includepdf[pages=-,fitpaper]{paper2}

And not to repeat yourself use this:

includepdfset{pages=-,fitpaper}
includepdf{paper1}
includepdf{paper2}
includepdf{paper3}
includepdf[fitpaper=false]{paper4} // you can add document specific options
includepdf{paper5}
includepdf{paper6}
includepdfset{} // to put default values back

Command Line

• pdftk

   $ pdftk 1.pdf 2.pdf 3.pdf cat output 123.pdf
  

• GhostScript

   $ gs -q -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=merged.pdf source1.pdf source2.pdf source3.pdf etc.pdf
  

  (via Macworld)

• PDFJAM is a suite of scripts that uses LaTeX and pdfpages on the backend.

   $ pdfjoin foo1.pdf foo2.pdf --outfile bar.pdf
  

  (via Uwe Hermann)

• stapler is a pure Python alternative to pdftk.

    $ stapler cat in1.pdf in2.pdf out.pdf
  

• PyMuPDF is a Python binding for MuPDF – “a lightweight PDF and XPS viewer”.

     $ python -m fitz join -o output.pdf file1.pdf file2.pdf
  

GUI

• Preview (Mac only) example

• Acrobat Pro (non-free) video example

• GUIPDFTK

• PDFCreator (Win only, free, Open Source, acts like a printer ⇒ no hyperlinks etc.)

• PDF Mod (Linux, free software)

• PDF-Shuffler (Linux, free software)

• PDFsam (JRE - Windows, Linux, Mac, free and non-free versions)

This question is very similar although the questioner didn't realize it.